I've found that it's very tedious to manage and choose my spells because I have to look in the list of the wizard/sorcerer spells that is sorted by level and for every spell, go and find it in the alphabetical list of every spell in the entire game to see if I want it or not and then write it down in a text document or something.

Pathfinder Spellbook I have found to be invaluable for looking up spell info during game; again it allows you to create a "favourites" list so you don't have to keep searching for individual spells by level.

Hero Lab is the most awesome solution. Sure, it's also a full character builder, but it lets you create a spellbook - the spell choosing is sorted by level and supports searching on keywords (e.g. Necromancy), and once you have your list you can quickly and directly access the spell descriptions from the spellbook list.

Since it's also a character builder it can also calculate your DCs, apply cast spells to your stats, etc. Costs $$ but is more than worth it. I've used it for every character for years now. Works on Mac and PC, with an iPad sheet viewer/roller.

There is! SRD Spellbook for iOS is a spell reference that lets you search or browse spells, as well as manage multiple characters' spell lists:

A complete spell reference guide for two of the most popular pen-and-paper roleplaying games, SRD Spellbook comes preloaded with all the spells from the 3.5 System Reference Document and the PF core and supplemental rulebooks, including the APG, and UM.

You can browse spells by name, class, or cleric domain, and search for spells by name or any text in the spell description. Spells cross-referenced in spell descriptions link directly to the referenced spell.

You can create and manage multiple named lists of spells. This can be used to keep lists of spells for multiple characters, or even a spellbook list and a prepared spells list for a single character.

SpellForge (site down as of Dec. 2014, but see below) is an excel spreadsheet that has most of the D&D 3.5 spells listed in it. The output spreadsheet has a short spell description, a reference to where the spell has come from and all of the important details (range, duration etc). It also lists your spells per day, calculates how many magic missiles you get due to your caster level etc. There is a space on the left of the output to tick whether or not you have studied/chosen a spell for the day. It is a good tool though not perfect.

d20Spellbook is a nice one. There is a Yahoo group that is adding more and more spells to it for both 3.5E and Pathfinder. You could take a look at Perram's Spellbook for Pathfinder to see if you can swap out the Pathfinder versions for 3.5E. It is nice as it makes spell cards so when you use a spell you just discard it from your hand.

The question mentions using Roll20 to run the game, so I feel it's worth pointing out the tools that have become available since the question was posted.

The May 2014 update, "Data Delve" introduced community-developed character sheets for Roll20. Users can submit sheets for any system to a GitHub repository; submissions which are approved are available to all users for use with their campaigns. (Mentor-level subscribers can also create "custom" sheets without needing to wait on the approval process.) As should be expected, there is a sheet available for D&D 3.5, which includes a spell list for each character. This should remove the need to have a third-party tool for keeping track of what spells are available to you.

The presentation of the spell list might not be perfect (I have not played 3.5 on Roll20, so I can't comment on the utility of the sheet's spell list, only that it's available), but Roll20's character sheets are open-source on GitHub and anyone can submit pull requests to improve things. Or, if your GM is a Mentor, you can have custom tweaks for just your campaign.

The June 2014 update also added a (subscriber-only) feature called "Character Vault" allowing users to save snapshots of a character, which could be used as backups or for transferring characters between games. This could also potentially be used for saving partial characters for things such as spellbooks.

The character sheets from the Data Delve update do not and cannot include things like the entire SRD's spell list. However, Q1 of 2015 will include the next major update, "Update of Holding" which, among other things, will have a "Compendium" tool. The Roll20 Compendium is slated to be an in-game reference lookup, including the openly available 3.5 SRD and Pathfinder SRD. Other systems will likely require discussion between the Roll20 team and the game's publisher, but 3.5 is the game that matters for this question, and the contents of its SRD are definitely targeted for availability early next year.

As an unreleased feature, fine details of the Roll20 Compendium are forthcoming. However, it has been announced as something that will definitely be included in the next major update. Currently, all signs point to the Roll20 Compendium removing the need to look up information from an external source (assuming the game system in question is included in the Compendium).

Nothing slows your game down more than a rules lookup. The Roll20 App will feature full support for our new Roll20 Compendium, a community-curated repository of information on the basics (such as spell definitions, stat blocks for the bestiary, class information, and more) of many game systems. Our intent is not to replace needing rule books, but rather to provide a complement to them; so when you see the “Fireball” spell on your Character Sheet and you can’t remember what the range is, a quick tap can tell you that information so you can get on with your game.

We’ll be starting with OGL-licensed information such as the Pathfinder SRD and 3.5 SRD, then working with publishers to expand this repository of helpful information in the future.

We’ll be unveiling more about this exciting new feature in a future blog post.

Website
Though not strictly an app, dndtools.eu is an excellent resource for 3.5 spells, feats, class and skills.

Regarding spells, you can search them using a "filter" which will allow you to search via sourcebook, class, level, school, sub-school; and much more. They have 3,900 spells on file, including 3.0 spells.

What I love about this site is they explicitly tell you exactly where to find the spell (what sourcebook and page number). This usually gets me to go and read the sourcebook, discovering new information I might not have known or considered previously.

I prefer to have a digital copy of my spellbook, and dndtools.eu makes it easy for me to copy the information into a word document and save it as a PDF. So once selected, I always have a quick reference for my spells in full detail.

Dndtools.eu only includes official WotC sourcebooks, so you don't have to worry about 3rd party or homebrew entries. The downside is Dragon Magazine isn't considered official, so nothing from there will be featured on the site.

Note: dndtools.eu does reference to items outside of the SRD. If linking to such sources is prohibited, I apologise.

iOS
I've never used it, but my brother swears by DnD Sheets. I believe you must manually enter the details for your spells. So it's useless in terms of spell searching, but good for a digital way to hold their information once you've decided on them.

dndtools is on the border of piracy due to its "don't use me if you don't have the manuals" disclaimer. WotC is known to have sent cease and discontinue letters to CrystalKeep, a site with the same policy. I'm not a lawyer but I'd say the site is contentious enough to be against the policies of RPG.SE. If you want to discuss this thing or just to get in touch with the community, join the Role-playing Games Chat!
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ZachielSep 28 '13 at 14:22

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As of late 2014 dndtool.eu has been shut down due to WotC taking legal action.
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SevenSidedDieDec 12 '14 at 18:17